Biogeographic dating of the Tetragnatha radiations on Hawaii

This work is yet unpublished. For more questions, please get in touch!

prepareGeogRangeData.R : Produces a Nexus file from biogeographic data partitionAlignment.py : Produces separate locus alignments from a concatenated a;ignment nonclock.Rev : Performs a non-clock analysis for use as a starting tree biogeogDating.Rev : Joint biogeographical and relaxed clock model for dating

Constraints

Root age ~ U(22.8, 34.0)

Notes:

• Landis' code produces 3 types of files

  • 1. parameter estimates for substitution model, relaxed clock and birth death models "run.log"
  • 2. stochastic character maps ("stoch.log")
  • 3. ancestral range maps ("states.log")

• Stochastic character mapping by rejection sampling (i.e, evolve states forward from root, only keep simulations with the same observed trait at tips; Nielsen 2002)

Files from Landis

make_anc_state.Rev

• Imports tree trace, calculates the maximum a posteriori (MAP) tree, the consensus tree and the maximi, clade credibility tree.
• Imports state log using

To do

• Inter-island distances (what is the distance used by landis to continental areas?)
• We will probably have to do model testing
  • Distance-weighted vs. not
  • UCLN clock vs. uexp?

Composes of the following models

Model 1 (M1):

• No biogeographic model + uniform root age prior of 0.1 - 15 Mya (split between viridis+versicolor and Hawaiians)

Model 2 (M2)

** Biogeographic model + uniform root age prior of 0.1 - 15 Mya (split between viridis+versicolor and Hawaiians)

Model 3 (M3)

** Clock model + no biogeography

Model 4 (M4)

** Clock model + biogeographic model

Loci used

Mitochondrial

• COI (2905-3322) coding
• CytB (2184-2539) coding
• 16S (2540-2904) coding
• 12S (1166-1524) coding

Nuclear

• ITS (1853-2183) non-coding
• 18S (1-269)
• SSU (796-1165)

2. Actin (270-495)
3. 28S (496-795)
4. H3 (1525-1852)